> I obtained the geometry from the RED server. Now I was wondering if
> I should use the amber99 atom types like MOL_p1.mol2 or
> apply gaff and use the MOL.mol2? Anyway in both cases I am getting
> some errors about missing parameters.

I would not use GAFF as this is a modified amino-acid.
Below are the FF atom types, which are corrected...

You could load leaprc.ff99SB and edit "DC" and "ALA" to get some ideas
about these FF atom types...

> Could you please suggest me how to correct them? and which option
> should I use?

> Urszula,
>
>> The RED runs are finished, for the sarin the calculations are
>> complete I guess, attached is obtained conformation
>> Mol_m1-o1-sm_sarin.mol2?.
>
> Seems ok to me; see the attached image...
>
> And using LEaP I get:
>
> Welcome to LEaP!
> (no leaprc in search path)
>> X = loadmol2 Mol_m1-o1-sm_sarin.mol2
> Loading Mol2 file: ./Mol_m1-o1-sm_sarin.mol2
> Reading MOLECULE named MOL
>> charge X
> Total unperturbed charge: -0.000000
> Total perturbed charge: -0.000000
>
>> However for the cyklosarin an error occurred, attached is log and
>> p2n files for the cyklosarin.
>> At the end of the cyklosarin file JOB1-gau_m1-1.com is:
>> Sum of Mulliken charges with hydrogens summed into heavy atoms = 0.00000
>> Error termination request processed by link 9999.
>> Error termination via Lnk1e in /usr/local/g09-userred/l9999.exe at
>> Wed Oct 24 19:34:57 2012.
>> Job cpu time: 1 days 8 hours 5 minutes 14.2 seconds.
>>
>> Do you know, what did go wrong? how can I avoid this error?
>
> The R.E.D. log reports:
>
> Geometry optimization(s) is/are being computed for molecule 1 ...
> [ FAILED ]
> See the file(s) "JOB1-gau_m1-1.out"
>
> Geometry optimization convergence problem
> Re-run the job using the best geometry obtained
>
> I think the structure did not converge in the Gaussian geometry
> optimization; you have to select the best (or the last) "Standard
> orientation" from the Gaussian log file; and copy the corresponding
> Cartesian coordinates in the P2N file and re-run R.E.D.; the format of
> the X, Y and Z columns in the P2N file does have to be strictly that
> of the PDB file format; thus you can do a crude copy/cut of these
> cart. coordinates taken from the Gaussian log into the P2N file...
>
> regards, Francois
>
>
>> Dear Urszula,
>>
>>> I run RED 2.0 I hope that the p2n file are ok now. Could you please
>>> have a look at them?
>>> The additional H were removed, and the P atom is asymmetric that is
>>> correct. The conformations of the
>>> sarin and cyklosarin were taken from the xray structures.
>>
>> Chemical equivalencing is correct this time.
>>
>> You use a single INTRA-MCC for the 2 capping groups; strictly, this is
>> correct, but this is not the 'Amber' approach, where an intra-mcc set
>> to zero is used for each capping group.
>>
>> Do you agree with the conformation you generated? is it in agreement
>> with experimental data? and/or is it the lowest minimum? an
>> alternative could be to split this whole molecule into two building
>> blocks.
>>
>> regards, Francois
>>
>>
>>> Dear Urszula,
>>>
>>>> I prepared two p2n files for RED server ( sarin and cykosarin).
>>>> However I am not quite sure if they are correct or I need to add
>>>> something else.
>>>
>>> You used Ante_R.E.D. 1.x to generate these P2N files; please use
>>> instead R.E.D. Server/Ante_R.E.D. 2.0 because Ante_R.E.D. 1.x does not
>>> handle chemical equivalencing between different chemical groups;
>>> See http://q4md-forcefieldtools.org/REDS/news.php>>> http://q4md-forcefieldtools.org/REDS/news.php#2>>> http://q4md-forcefieldtools.org/REDS/popup/popanteredtopequiv.php>>>
>>> For Sarin, the two terminal methyl groups in the side chain should be
>>> equivalenced; i.e. they should bear both the following names: CT16 H16
>>> H16 H16 or both CT17 H17 H17 H17
>>>
>>> For cyclosarin, same type of remarks for the methylene group in the
>>> pseudo cyclohexane group: CT15 and CT19 should bear the same number;
>>> same remark for CT16 and CT18.
>>> You have two additional hydrogen atoms in this dipeptide; I am not
>>> sure this is correct...
>>>
>>> then, I would check that the optimized geometry for each of these
>>> dipeptides corresponds to what I want after geometry optimization.
>>>
>>> finally, is your P atom asymmetric?
>>>
>>> regards, Francois